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3.  Pandemic Vibrio parahaemolyticus, Maryland, USA, 2012 
Emerging Infectious Diseases  2014;20(4):718-720.
doi:10.3201/eid2004.130818
PMCID: PMC3966373  PMID: 24655659
bacteria; pandemic; Vibrio parahaemolyticus; Maryland; USA; United States; cross contamination; food preparation; traceback; PFGE pattern; pulsed-field gel electrophoresis pattern; seafood; epidemiology; gastroenteritis
4.  ATR Suppresses Endogenous DNA Damage and Allows Completion of Homologous Recombination Repair 
PLoS ONE  2014;9(3):e91222.
DNA replication fork stalling or collapse that arises from endogenous damage poses a serious threat to genome stability, but cells invoke an intricate signaling cascade referred to as the DNA damage response (DDR) to prevent such damage. The gene product ataxia telangiectasia and Rad3-related (ATR) responds primarily to replication stress by regulating cell cycle checkpoint control, yet it’s role in DNA repair, particularly homologous recombination (HR), remains unclear. This is of particular interest since HR is one way in which replication restart can occur in the presence of a stalled or collapsed fork. Hypomorphic mutations in human ATR cause the rare autosomal-recessive disease Seckel syndrome, and complete loss of Atr in mice leads to embryonic lethality. We recently adapted the in vivo murine pink-eyed unstable (pun) assay for measuring HR frequency to be able to investigate the role of essential genes on HR using a conditional Cre/loxP system. Our system allows for the unique opportunity to test the effect of ATR loss on HR in somatic cells under physiological conditions. Using this system, we provide evidence that retinal pigment epithelium (RPE) cells lacking ATR have decreased density with abnormal morphology, a decreased frequency of HR and an increased level of chromosomal damage.
doi:10.1371/journal.pone.0091222
PMCID: PMC3968013  PMID: 24675793
5.  Impaired CD4+ and T-helper 17 cell memory response to Streptococcus pneumoniae is associated with elevated glucose and percent glycated hemoglobin A1c in Mexican Americans with type 2 diabetes mellitus 
Individuals with type 2 diabetes are significantly more susceptible to pneumococcal infections than healthy individuals of the same age. Increased susceptibility is the result of impairments in both innate and adaptive immune systems. Given the central role of T-helper 17 (Th17) and T-regulatory (Treg) cells in pneumococcal infection and their altered phenotype in diabetes, this study was designed to analyze the Th17 and Treg cell responses to a whole heat-killed capsular type 2 strain of Streptococcus pneumoniae. Patients with diabetes demonstrated a lower frequency of total CD+T-cells, which showed a significant inverse association with elevated fasting blood glucose. Measurement of specific subsets indicated that those with diabetes had, low intracellular levels of interleukin (IL)-17, and lower pathogen-specific memory CD4+ and IL-17+ cell numbers. No significant difference was observed in the frequency of CD4+ and Th17 cells between those with and without diabetes. However, stratification of data by obesity indicated a significant increase in frequency of CD4+ and Th17 cells in obese individuals with diabetes compared with nonobese individual with diabetes. The memory CD+T-cell response was associated inversely with both fasting blood glucose and percent glycated hemoglobin A1c. This study demonstrated that those with type 2 diabetes have a diminished pathogen-specific memory CD4+ and Th17 response, and low percentages of CD+T-cells in response to S. pneumoniae stimulation.
doi:10.1016/j.trsl.2013.07.005
PMCID: PMC3954646  PMID: 23927943
6.  Sustained Effects of the Communities That Care System on Prevention Service System Transformation 
American journal of public health  2012;103(3):529-535.
Objectives
We examined whether the Communities That Care (CTC) system sustained effects 1.5 years after study funding ended on prevention system constructs expected to be important for community-level reductions in drug use and antisocial behaviors among youths.
Methods
Data were from a community trial of 24 towns in the United States randomized to either the CTC intervention or control conditions. Participants were 928 community key leaders interviewed at 1 to 4 waves from 2001 to 2009. Intervention activities, including training and technical assistance, were conducted between 2003 and 2008 in the CTC communities.
Results
Leaders from CTC communities reported higher levels of adoption of a science-based approach to prevention and a higher percentage of funding desired for prevention activities in 2009 than did leaders in control communities. CTC communities showed a higher increase over time in community norms against adolescent drug use as well as adoption of a science-based approach compared with control communities.
Conclusions
These findings indicated that CTC implementation produced enduring transformation of important prevention system constructs in intervention communities, which might, in turn, produce long-term reductions in youth problem behaviors.
doi:10.2105/AJPH.2011.300567
PMCID: PMC3673484  PMID: 22720764
7.  Differentially regulated gene expression associated with hepatitis C virus clearance 
The Journal of General Virology  2013;94(Pt 3):534-542.
Human chronic hepatitis C virus (HCV) infections pose a significant public health threat, necessitating the development of novel treatments and vaccines. HCV infections range from spontaneous resolution to end-stage liver disease. Approximately 10–30 % of HCV infections undergo spontaneous resolution independent of treatment by yet-to-be-defined mechanisms. These individuals test positive for anti-HCV antibodies in the absence of detectable viral serum RNA. To identify genes associated with HCV clearance, this study compared gene expression profiles between current drug users chronically infected with HCV and drug users who cleared their HCV infection. This analysis identified 91 differentially regulated (up- or downregulated by twofold or more) genes potentially associated with HCV clearance. The majority of genes identified were associated with immune function, with the remaining genes categorized either as cancer related or ‘other’. Identification of factors and pathways that may influence virus clearance will be essential to the development of novel treatment strategies.
doi:10.1099/vir.0.047738-0
PMCID: PMC3709607  PMID: 23152368
8.  The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes 
PLoS Computational Biology  2014;10(2):e1003469.
Over repeat presentations of the same stimulus, sensory neurons show variable responses. This “noise” is typically correlated between pairs of cells, and a question with rich history in neuroscience is how these noise correlations impact the population's ability to encode the stimulus. Here, we consider a very general setting for population coding, investigating how information varies as a function of noise correlations, with all other aspects of the problem – neural tuning curves, etc. – held fixed. This work yields unifying insights into the role of noise correlations. These are summarized in the form of theorems, and illustrated with numerical examples involving neurons with diverse tuning curves. Our main contributions are as follows. (1) We generalize previous results to prove a sign rule (SR) — if noise correlations between pairs of neurons have opposite signs vs. their signal correlations, then coding performance will improve compared to the independent case. This holds for three different metrics of coding performance, and for arbitrary tuning curves and levels of heterogeneity. This generality is true for our other results as well. (2) As also pointed out in the literature, the SR does not provide a necessary condition for good coding. We show that a diverse set of correlation structures can improve coding. Many of these violate the SR, as do experimentally observed correlations. There is structure to this diversity: we prove that the optimal correlation structures must lie on boundaries of the possible set of noise correlations. (3) We provide a novel set of necessary and sufficient conditions, under which the coding performance (in the presence of noise) will be as good as it would be if there were no noise present at all.
Author Summary
Sensory systems communicate information to the brain — and brain areas communicate between themselves — via the electrical activities of their respective neurons. These activities are “noisy”: repeat presentations of the same stimulus do not yield to identical responses every time. Furthermore, the neurons' responses are not independent: the variability in their responses is typically correlated from cell to cell. How does this change the impact of the noise — for better or for worse? Our goal here is to classify (broadly) the sorts of noise correlations that are either good or bad for enabling populations of neurons to transmit information. This is helpful as there are many possibilities for the noise correlations, and the set of possibilities becomes large for even modestly sized neural populations. We prove mathematically that, for larger populations, there are many highly diverse ways that favorable correlations can occur. These often differ from the noise correlation structures that are typically identified as beneficial for information transmission – those that follow the so-called “sign rule.” Our results help in interpreting some recent data that seems puzzling from the perspective of this rule.
doi:10.1371/journal.pcbi.1003469
PMCID: PMC3937411  PMID: 24586128
9.  Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli 
PLoS Genetics  2014;10(2):e1004120.
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.
Author Summary
Genome-wide genetic interaction (GI) screens have been performed in yeast, but no analogous large-scale studies have yet been reported for bacteria. Here, we have used E. coli synthetic genetic array (eSGA) technology developed by our group to quantitatively map GIs to reveal epistatic dependencies and functional cross-talk among ∼600,000 digenic mutant combinations. By combining this epistasis information with functional modules derived by our group's earlier efforts from proteomic and genomic context (GC)-based methods, we identify several unexpected pathway-level dependencies, functional links between protein complexes, and biological roles of uncharacterized bacterial gene products. As part of the study, two of our pathway predictions from GI screens were validated experimentally, where we confirmed the role of these new components in iron-sulphur biogenesis and ribosome integrity. We also extrapolated the epistatic connectivity diagram of E. coli to 233 distantly related γ-proteobacterial species lacking GI information, and identified co-conserved genes and functional modules important for bacterial pathogenesis. Overall, this study describes the first genome-scale map of GIs in gram-negative bacterium, and through integrative analysis with previously derived protein-protein and GC-based interaction networks presents a number of novel insights into the architecture of bacterial pathways that could not have been discerned through either network alone.
doi:10.1371/journal.pgen.1004120
PMCID: PMC3930520  PMID: 24586182
10.  The Cytotoxicity of Aflatoxin B1 in Human Lymphocytes 
Objectives:
Aflatoxin B1 (AFB1) is a naturally occurring carcinogenic and immunosuppressive compound. This study was designed to measure its toxic effects on human peripheral blood mononuclear cells (PBMC).
Methods:
The study recruited 7 healthy volunteers. PBMC were isolated and cellular respiration was monitored using a phosphorescence oxygen analyser. The intracellular caspase activity was measured by the caspase-3 substrate N-acetyl-asp-glu-val-asp-7-amino-4-methylcoumarin. Phosphatidylserine exposure and membrane permeability to propidium iodide (PI) were measured by flow cytometry.
Results:
Cellular oxygen consumption was inhibited by 2.5 μM and 25 μM of AFB1. Intracellular caspase activity was noted after two hours of incubation with 100 μM of AFB1. The number of Annexin V-positive cells increased as a function of AFB1 concentration and incubation time. At 50 μM, a significant number of cells became necrotic after 24 hours (Annexin V-positive and PI-positive).
Conclusion:
The results show AFB1 is toxic to human lymphocytes and that its cytotoxicity is mediated by apoptosis and necrosis.
PMCID: PMC3916279  PMID: 24516756
Aflatoxin B1; Oxygen Analyzer; Cellular Respiration; Mitochondria; Caspases; Leukocytes, Mononuclear
11.  When do microcircuits produce beyond-pairwise correlations? 
Describing the collective activity of neural populations is a daunting task. Recent empirical studies in retina, however, suggest a vast simplification in how multi-neuron spiking occurs: the activity patterns of retinal ganglion cell (RGC) populations under some conditions are nearly completely captured by pairwise interactions among neurons. In other circumstances, higher-order statistics are required and appear to be shaped by input statistics and intrinsic circuit mechanisms. Here, we study the emergence of higher-order interactions in a model of the RGC circuit in which correlations are generated by common input. We quantify the impact of higher-order interactions by comparing the responses of mechanistic circuit models vs. “null” descriptions in which all higher-than-pairwise correlations have been accounted for by lower order statistics; these are known as pairwise maximum entropy (PME) models. We find that over a broad range of stimuli, output spiking patterns are surprisingly well captured by the pairwise model. To understand this finding, we study an analytically tractable simplification of the RGC model. We find that in the simplified model, bimodal input signals produce larger deviations from pairwise predictions than unimodal inputs. The characteristic light filtering properties of the upstream RGC circuitry suppress bimodality in light stimuli, thus removing a powerful source of higher-order interactions. This provides a novel explanation for the surprising empirical success of pairwise models.
doi:10.3389/fncom.2014.00010
PMCID: PMC3915758  PMID: 24567715
retinal ganglion cells; maximum entropy distribution; stimulus-driven; correlations; computational model
12.  Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5− Strain Isolated from Chicken Breast 
Genome Announcements  2013;1(6):e01068-13.
Salmonella enterica subsp. enterica serovar Typhimurium is a leading cause of salmonellosis. Here, we report a closed genome sequence, including sequences of 3 plasmids, of Salmonella serovar Typhimurium var. 5− CFSAN001921 (National Antimicrobial Resistance Monitoring System [NARMS] strain ID N30688), which was isolated from chicken breast meat and shows resistance to 10 different antimicrobials. Whole-genome and plasmid sequence analyses of this isolate will help enhance our understanding of this pathogenic multidrug-resistant serovar.
doi:10.1128/genomeA.01068-13
PMCID: PMC3868858  PMID: 24356834
13.  Early Effects of Communities That Care on Targeted Risks and Initiation of Delinquent Behavior and Substance Use 
Purpose
Communities That Care (CTC) is a prevention system designed to reduce levels of adolescent delinquency and substance use through the selection and use of effective preventive interventions tailored to a community’s specific profile of risk and protection. This article describes early findings from the first group-randomized trial of CTC.
Methods
A panel of 4407 fifth-grade students was surveyed annually through seventh grade. Analyses were conducted to assess the effects of CTC on reducing levels of targeted risk factors and reducing initiation of delinquent behavior and substance use in seventh grade, 1.67 years after implementing preventive interventions selected through the CTC process.
Results
Mean levels of targeted risks for students in seventh grade were significantly lower in CTC communities compared with controls. Significantly fewer students in CTC communities than in control communities initiated delinquent behavior between grades 5 and 7. No significant intervention effect on substance use initiation by spring of seventh grade was observed.
Conclusions
CTC’s theory of change hypothesizes that it takes from 2 to 5 years to observe community-level effects on risk factors and 5 or more years to observe effects on adolescent delinquency or substance use. The early findings indicating hypothesized effects of CTC on targeted risk factors and initiation of delinquent behavior are promising.
doi:10.1016/j.jadohealth.2008.01.022
PMCID: PMC3867289  PMID: 18565433
Delinquency; Substance use; Adolescents; Intervention; Prevention science
14.  High-throughput, multiplexed IgG subclassing of antigen-specific antibodies from clinical samples 
Journal of immunological methods  2012;386(1-2):117-123.
In vivo, the activity of antibodies relies critically on properties of both the variable domain, responsible for antigen recognition, and the constant domain, responsible for innate immune recognition. Here, we describe a flexible, microsphere-based array format for capturing information about both functional ends of disease-specific antibodies from complex, polyclonal clinical serum samples. Using minimal serum, we demonstrate IgG subclass profiling of multiple antibody specificities. We further capture and determine the subclass of epitope-specific antibodies. The data generated in this array provides a profile of the humoral immune response with multi-dimensional metrics regarding properties of both variable and constant IgG domains. Significantly, these properties are assessed simultaneously, and therefore information about the relationship between variable and constant domain characteristics is captured, and can be used to predict functions such as antibody effector activity.
doi:10.1016/j.jim.2012.09.007
PMCID: PMC3475184  PMID: 23023091
antibody; IgG subclass; clinical samples; humoral immunity
15.  Predictive Validity of Established Cut Points for Risk and Protective Factor Scales from the Communities That Care Youth Survey 
The journal of primary prevention  2012;33(5-6):249-258.
Community coalitions are a popular strategy to coordinate activities and resources to prevent adolescent substance use and delinquent behavior. Despite early evidence of their lack of effectiveness, a new generation of community coalitions has shown positive results in preventing youth substance use and delinquency. This success can be attributed to coalition decision making focused on reducing local risk factors and increasing local protective factors through the use of evidence-based prevention programs. A previous study using cross-sectional data established cut point values for scales measuring risk and protective factors on the Communities That Care Youth Survey (CTCYS) to identify high levels of risk and low levels of protection in communities on each scale. The current study extended this previous research by using longitudinal data to assess the validity of risk and protective factor cut point values in predicting substance use and delinquent behavior 1 year after risk and protection were measured. The findings demonstrate the predictive validity of cut points for risk and protective factor scales measured by the CTCYS and suggest their utility in guiding prevention efforts.
doi:10.1007/s10935-012-0280-1
PMCID: PMC3531995  PMID: 23143070
Risk factors; Protective factors; Substance use; Youth surveys
16.  Clinical Significance of Methicillin-Resistant Staphylococcus aureus Colonization on Hospital Admission: One-Year Infection Risk 
PLoS ONE  2013;8(11):e79716.
Background
Methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization among inpatients is a well-established risk factor for MRSA infection during the same hospitalization, but the long-term risk of MRSA infection is uncertain. We performed a retrospective cohort study to determine the one-year risk of MRSA infection among inpatients with MRSA-positive nasal polymerase chain reaction (PCR) tests confirmed by positive nasal culture (Group 1), patients with positive nasal PCR but negative nasal culture (Group 2), and patients with negative nasal PCR (Group 3).
Methodology/Principal Findings
Subjects were adults admitted to a four-hospital system between November 1, 2006 and March 31, 2011, comprising 195,255 admissions. Patients underwent nasal swab for MRSA PCR upon admission; if positive, nasal culture for MRSA was performed; if recovered, MRSA was tested for Panton-Valentine Leukocidin (PVL). Outcomes included MRSA-positive clinical culture and skin and soft tissue infection (SSTI). Group 1 patients had a one-year risk of MRSA-positive clinical culture of 8.0% compared with 3.0% for Group 2 patients, and 0.6% for Group 3 patients (p<0.001). In a multivariable model, the hazard ratios for future MRSA-positive clinical culture were 6.52 (95% CI, 5.57 to 7.64) for Group 1 and 3.40 (95% CI, 2.70 to 4.27) for Group 2, compared with Group 3 (p<0.0001). History of MRSA and concurrent MRSA-positive clinical culture were significant risk factors for future MRSA-positive clinical culture. Group 1 patients colonized with PVL-positive MRSA had a one-year risk of MRSA-positive clinical culture of 10.1%, and a one-year risk of MRSA-positive clinical culture or SSTI diagnosis of 21.7%, compared with risks of 7.1% and 12.5%, respectively, for patients colonized with PVL-negative MRSA (p = 0.04, p = 0.005, respectively).
Conclusions/Significance
MRSA nasal colonization is a significant risk factor for future MRSA infection; more so if detected by culture than PCR. Colonization with PVL-positive MRSA is associated with greater risk than PVL-negative MRSA.
doi:10.1371/journal.pone.0079716
PMCID: PMC3835821  PMID: 24278161
17.  Bile Salt Inhibition of Host Cell Damage by Clostridium Difficile Toxins 
PLoS ONE  2013;8(11):e79631.
Virulent Clostridium difficile strains produce toxin A and/or toxin B that are the etiological agents of diarrhea and pseudomembranous colitis. Treatment of C. difficile infections (CDI) has been hampered by resistance to multiple antibiotics, sporulation, emergence of strains with increased virulence, recurrence of the infection, and the lack of drugs that preserve or restore the colonic bacterial flora. As a result, there is new interest in non-antibiotic CDI treatments. The human conjugated bile salt taurocholate was previously shown in our laboratory to inhibit C. difficile toxin A and B activities in an in vitro assay. Here we demonstrate for the first time in an ex vivo assay that taurocholate can protect Caco-2 colonic epithelial cells from the damaging effects of the C. difficile toxins. Using caspase-3 and lactate dehydrogenase assays, we have demonstrated that taurocholate reduced the extent of toxin B-induced apoptosis and cell membrane damage. Confluent Caco-2 cells cultured with toxin B induced elevated caspase-3 activity. Remarkably, addition of 5 mM taurocholate reduced caspase-3 activity in cells treated with 2, 4, 6, and 12 µg/ml of toxin B by 99%, 78%, 64%, and 60%, respectively. Furthermore, spent culture medium from Caco-2 cells incubated with both toxin B and taurocholate exhibited significantly decreased lactate dehydrogenase activity compared to spent culture medium from cells incubated with toxin B only. Our results suggest that the mechanism of taurocholate-mediated inhibition functions at the level of toxin activity since taurocholate did not affect C. difficile growth and toxin production. These findings open up a new avenue for the development of non-antibiotic therapeutics for CDI treatment.
doi:10.1371/journal.pone.0079631
PMCID: PMC3823588  PMID: 24244530
18.  Generation of a Novel, Cox2-Targeted, Interferon-Expressing, Conditionally-Replicative Adenovirus for Pancreatic Cancer Therapy 
American journal of surgery  2012;204(5):741-750.
Background
Oncolytic adenoviruses provide a promising alternative for cancer treatment. Recently, adjuvant α-interferon has shown significant survival benefits for pancreatic cancer, yet was impeded by systemic toxicity. To circumvent these problems adenovirus with high-level targeted IFNα expression can be generated.
Methods
Conditionally replicative adenoviruses (CRAds) with improved virulence and selectivity for pancreatic cancer were generated. The vectors were tested in vitro, in vivo, and in human pancreatic cancer and normal tissue specimens.
Results
Adenoviral death protein and fiber modifications significantly improved oncolysis. CRAds selectively replicated in vitro, in vivo and showed persistent spread in cancer xenografts. They exhibited high-level replication in human pancreatic cancer specimens, but not in normal tissues. Improved IFN-CRAd oncolytic efficiency was demonstrated.
Conclusions
Optimized Cox2CRAds show highly favorable effects in vitro and in vivo. We have the first report of a pancreatic cancer specific, highly virulent, IFN-expressing CRAd and believe this strategy to have great promise.
doi:10.1016/j.amjsurg.2012.02.016
PMCID: PMC3467355  PMID: 22748294
Pancreatic cancer; Oncolytic virus; Adenovirus; Conditionally replicative adenovirus (CRAd); Gene therapy; Interferon alpha; Adenoviral death protein (ADP); Cox2; Krumdiek tissue slicer
19.  Phylogenomic Analysis Identifies Gene Gains That Define Salmonella enterica Subspecies I 
PLoS ONE  2013;8(10):e76821.
Comparative methods for analyzing whole genome sequence (WGS) data enable us to assess the genetic information available for reconstructing the evolutionary history of pathogens. We used the comparative approach to determine diagnostic genes for Salmonella enterica subspecies I. S. enterica subsp. I strains are known to infect warm-blooded organisms regularly while its close relatives tend to infect only cold-blooded organisms. We found 71 genes gained by the common ancestor of Salmonella enterica subspecies I and not subsequently lost by any member of this subspecies sequenced to date. These genes included many putative functional phenotypes. Twenty-seven of these genes are found only in Salmonella enterica subspecies I; we designed primers to test these genes for use as diagnostic sequence targets and data mined the NCBI Sequence Read Archive (SRA) database for draft genomes which carried these genes. We found that the sequence specificity and variability of these amplicons can be used to detect and discriminate among 317 different serovars and strains of Salmonella enterica subspecies I.
doi:10.1371/journal.pone.0076821
PMCID: PMC3810377  PMID: 24204679
20.  Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters 
Genome Biology and Evolution  2013;5(11):2109-2123.
The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles—some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.
doi:10.1093/gbe/evt159
PMCID: PMC3845640  PMID: 24158624
H antigens; serovar; O antigens; CRISPR; lineage-through-time plot; comparative method
21.  Novel Staphylococcal Glycosyltransferases SdgA and SdgB Mediate Immunogenicity and Protection of Virulence-Associated Cell Wall Proteins 
PLoS Pathogens  2013;9(10):e1003653.
Infection of host tissues by Staphylococcus aureus and S. epidermidis requires an unusual family of staphylococcal adhesive proteins that contain long stretches of serine-aspartate dipeptide-repeats (SDR). The prototype member of this family is clumping factor A (ClfA), a key virulence factor that mediates adhesion to host tissues by binding to extracellular matrix proteins such as fibrinogen. However, the biological siginificance of the SDR-domain and its implication for pathogenesis remain poorly understood. Here, we identified two novel bacterial glycosyltransferases, SdgA and SdgB, which modify all SDR-proteins in these two bacterial species. Genetic and biochemical data demonstrated that these two glycosyltransferases directly bind and covalently link N-acetylglucosamine (GlcNAc) moieties to the SDR-domain in a step-wise manner, with SdgB appending the sugar residues proximal to the target Ser-Asp repeats, followed by additional modification by SdgA. GlcNAc-modification of SDR-proteins by SdgB creates an immunodominant epitope for highly opsonic human antibodies, which represent up to 1% of total human IgG. Deletion of these glycosyltransferases renders SDR-proteins vulnerable to proteolysis by human neutrophil-derived cathepsin G. Thus, SdgA and SdgB glycosylate staphylococcal SDR-proteins, which protects them against host proteolytic activity, and yet generates major eptopes for the human anti-staphylococcal antibody response, which may represent an ongoing competition between host and pathogen.
Author Summary
Staphylococcus aureus and S. epidermidis are major bacterial pathogens that can cause life-threatening human diseases. Following entry into the circulation, S.aureus can infect virtually any organ. However, it must first counter antibacterial mechanisms of the innate immune system, including those involving macrophages and neutrophils. Important for staphylococcal adhesion to and successful colonization of host tissues, is a family of bacterial surface proteins containing multiple repeats of serine-aspartate repeats (SDR) adjacent to an adhesive A-domain. The biological functions of the SDR-domain of these SDR proteins remain elusive. We found that the SDR-domain of all staphylococcal SDR proteins is heavily glycosylated. We identified two novel glycosylases, SdgA and SdgB, which are responsible for glycosylation in two steps, and found that this glycosylation protects the adhesive SDR proteins against proteolytic attack by human neutrophil cathepin G. Since pathogen binding to human tissues, including the extracellular matrix protein fibrinogen, depends on SDR proteins, this glycosylation may be important for successful colonization of the human host. We also show that the SdgB-mediated glycosylation creates an immunodominant epitope for highly opsonic antibodies in humans. These antibodies account for a significant proportion of the total anti-staphylococcal IgG response.
doi:10.1371/journal.ppat.1003653
PMCID: PMC3794999  PMID: 24130480
22.  Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their Pathogenicity 
Genome Announcements  2013;1(5):e00805-13.
We sequenced the genomes of two strains of O104:H21 enterohemorrhagic Escherichia coli (EHEC) isolated during an outbreak of hemorrhagic colitis in Montana in 1994. These strains carried a plasmid that contains several virulence genes not present in pO157. The genome sequences will improve phylogenetic analysis of other non-O157 E. coli strains in the future.
doi:10.1128/genomeA.00805-13
PMCID: PMC3790099  PMID: 24092795
23.  Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic Resistance 
Genome Announcements  2013;1(5):e00806-13.
The Salmonella enterica strains that are representatives of the S. enterica serovar Typhimurium complex in reference collection A (SARA) are closely related but exhibit differences in antibiotic resistance, which could have public health consequences. To better understand the mechanisms behind these resistances, we sequenced the genomes of two multidrug-resistant strains: SARA64 (Muenchen) and SARA33 (Heidelberg).
doi:10.1128/genomeA.00806-13
PMCID: PMC3790100  PMID: 24092796
24.  Colonization and Internalization of Salmonella enterica in Tomato Plants 
The consumption of fresh tomatoes has been linked to numerous food-borne outbreaks involving various serovars of Salmonella enterica. Recent advances in our understanding of plant-microbe interactions have shown that human enteric pathogenic bacteria, including S. enterica, are adapted to survive in the plant environment. In this study, tomato plants (Solanum lycopersicum cv. Micro-Tom) grown in sandy loam soil from Virginia's eastern shore (VES) were inoculated with S. enterica serovars to evaluate plausible internalization routes and to determine if there is any niche fitness for certain serovars. Both infested soil and contaminated blossoms can lead to low internal levels of fruit contamination with Salmonella. Salmonella serovars demonstrated a great ability to survive in environments under tomato cultivation, not only in soil but also on different parts of the tomato plant. Of the five serovars investigated, Salmonella enterica serovars Newport and Javiana were dominant in sandy loam soil, while Salmonella enterica serovars Montevideo and Newport were more prevalent on leaves and blossoms. It was also observed that Salmonella enterica serovar Typhimurium had a poor rate of survival in all the plant parts examined here, suggesting that postharvest contamination routes are more likely in S. Typhimurium contamination of tomato fruit. Conversely, S. Newport was the most prevalent serovar recovered in both the tomato rhizosphere and phyllosphere. Plants that were recently transplanted (within 3 days) had an increase in observable internalized bacteria, suggesting that plants were more susceptible to internalization right after transplant. These findings suggest that the particular Salmonella serovar and the growth stage of the plant were important factors for internalization through the root system.
doi:10.1128/AEM.03704-12
PMCID: PMC3623171  PMID: 23377940
25.  Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere 
PLoS ONE  2013;8(9):e73079.
The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.
doi:10.1371/journal.pone.0073079
PMCID: PMC3767688  PMID: 24039862

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